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>ENSCAPT00000000001.1 cdna (...)
CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTG
...
GAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCAT
ACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCC
TTTGGATGTAGCA

#Open data file;
chomp($paths[1]);
...
    }
}
print "$_ $count{$_}\n" for sort keys %count;

#!/usr/bin/env perl -l

...
GAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCAT
ACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCC
TTTGGATGTAGCA

KEY=|ENSCAPT00000000001.1 cdna (...)|
SEQ=|CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTGCCATT
+CCGGCGTTACAATGGTGGAGTTGGAAGGTGTGCCCAGGCCAAACAATGGGGCTGGACCCAGGGTCGGTG
+GCCCAAAAAGAGTGCTGAATTTTTGCTGCAC|
...
SEQ=|CAGCTGCTGAAGACGGAGCTGGGGTCCTTCTTCACCGAGTACCTGCAGAACCAGCTGCTGACCAA
+AGGCATGGTGATCCTTCGGGACAAGATCCGCTTCTATGAGGGACAGAAACTGCTGGACTCGCTGGCAGA
+GACCTGGGACTTCTTCTTCAGCGACGTGCTGCCCACGCTGCAGGCCATCTTCTACCC|
KEY=|ENSCAPT00000000004.1 cdna (...)|
SEQ=|ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCCTGCTC
+GGCTGACGAGGTGCAGCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAAGGTATTTGTTTCAT
+CTACACCAGAGAAGGCAGACCGAGTGGCGAGGCTTTTGTTGAACTTGAATCCGAAGATGAAGTCAAACT
+ATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACACGGCCAATGA
+TGGCTTTGTACGGCTTAGAGAACTCCCCTTTGGATGTAGCA|

%count = ();